User talk:Eran Hodis/talkarchive/080619

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Hey Eran,

Thanks for the input on 2veo, I'm sure you're right that keeping the Structure Box is a good idea. It's still pretty much work in progress though, and I was wondering about a few things: is it possible to have the "initial scene" link take you back to the view such as it is when first loading the page, and not the one generated from the PDB? Can the zoom-level be set numerically or is that something you do strictly with the scene-editor? Thanks! /Daniel

--- Dear Eran,

The email tag trick is interesting and I didn't know about it. However, it seems to me that it would not protect the email address since it remains in a form recognizable to worms in the page source and any user can view source too. I don't worry about my own email. I started putting it plainly in all my web pages in 1995, and I continue to do so. At this point, the spam control on my email system is so good that it causes no problem. However, I try to be careful never to put anyone else's email on a website in plain form. Eric Martz

Eran- Let's see how my attempts to figure out "user talk" go. I have been meaning to get back to you for a long time, but as you can see, it hasn't happened until now. It was a good experience to work on Proteopedia and interesting how the page I made would change without me knowing it as things were worked out on your end. Karl shared with me how you have been sharing the Photosystem II page in Italy. It was surprising to me to find that others were interested in seeing it too, but that's the point of it all! The interface Proteopedia has for J-mol is definitely better than many others. My classmates were all jealous that I got to use Proteopedia and they had to use other, more clunky interfaces. One thing that I attempted and couldn't figure out was labeling. Photosystem II has a lot of ligands and my attempts to label them as well as other individual atoms resulted in the labeling of every atom! Maybe I was just missing something, but that could be something to work on. Another feature which might be helpful would be a representations "reset" button. Sometimes, I would try things and then not like them, but since the original settings aren't given, it took a more round about approach to return to the original view. Reset would just make things easier. Thanks for letting me be a part of Proteopedia. -Emily Forschler Emily Forschler 17:48, 3 June 2008 (EDT)

Dear Eran, please see Sandbox 30. We uploaded a file from PQS. The filename is 1nsb_mmol.pdb. We tried to display it in Jmol on Sandbox 30 but failed. Please help us, thanks, -Eric in Osaka

Hi Eran, I was wanting to delete the extra "Tom Garrett" page but could not see ho to delete a page Is this possible... Tom

Hey Eran, we were locked in the discussion hall, would you have time tomorrow at coffee break 11am? Nicole Pendini

getting technical now (does this work)? Nicole R Pendini 11:07, 7 June 2008 (IDT)

Hi Eran,

How are you? My flight home was quite ok, sleeping! How about yours? And of course I miss Erice very very much... :( Please send me the photo!!! I will put my pictures somewhere in the net and send you the link...

My 2p18 page is not finished... I will add some more info on the structure and of course I would like to add some more pictures... I will have a look on the tutorial! Thanks!:) I am really enjoying proteopedia!!:D Even a professor can do it, right?!

So... you just watch every page on proteopedia?!?!

Lidia

Hi Eran, User talk is starting to make sense now. How is the time stamp put on? I see some notes are stamped and others are not.

I remember now that I had colored the background black of one the links using SAT, but I had forgotten that I had done that. Things drop out of my mind so quickly unless I do them several times.

Karl Oberholser

Green links disappear
Eran, Several times I have had the green links disappear after I make some changes. I can not see anything that is wrong with the code. After changing this and that it comes back, but I have never discovered anyone thing that consistently causes it to return. A current example is in the Ramachandran page under the Psi torsional angle section. In the first line there should be a green link between the double 'to to'.

Karl Oberholser 16:59, 12 June 2008 (IDT)

Dihedral angles
Eran,

Thanks for the reminder. I used that measurement several months ago, but forgot about it. Actually I got distracted by the selection that is on the Jmol right-mouse click menu. If you turn on the measurement from the menu and also select 'Click for torsional measurement', you can measure the value of the angle by single clicking on the four atoms making up the angle. I was not able to find the comparable commands which I could use in the console. I did stumble across and was reminded of the double clicking technique. I now have in the tutorial a statement describing how to do that.

Karl Oberholser 16:16, 13 June 2008 (IDT)

Inserting applet
Eran,

Using STRUCTURE_3cin | PDB=3cin  |  SCENE=  in cased in double braces permits one to use a particular scene when the applet is inserted. I am using a file that does not have a PDB ID. Can a scene be used with this method of insertion <applet load='file.pdb' size='300' frame='true' ? Or is there some other way of having a particular scene appear when the applet is first inserted?

Karl Oberholser 23:04, 17 June 2008 (IDT)

User pages
Eran,

Thanks for making those links. That is the expected thing to do, but it did not cross my mind at the time.

Karl Oberholser 20:51, 18 June 2008 (IDT)